This is an automated email from the ASF dual-hosted git repository.
lahirujayathilake pushed a change to branch master
in repository https://gitbox.apache.org/repos/asf/airavata.git
from c965eb82e5 Merge pull request #455 from
apache/agent-framewok-refactoring
new 95b508db6d CyberFaCES docker file
new 397f1cdaf6 add file ops to jupyter magics, cleanup code, update
agent.sh
new 741815f673 temp commit to get cyberfaces meeting poc
new 896f11c016 update data tar and analysis script
new 684711d180 add airavata magics to dev-tools/, make airavata-agent/
build generic
new 9394c945fd reorganize agent-framework related code. make
airavata-magics a python package.
new 17012d556b revise jupyterhub spawned notebooks, add makefiles
new 3560c00c2d initial experiment sdk implementation
new 8b9cacf758 improve auth flow, add python code invocation, add plan
crud apis and file ul/dl apis, reduce settings.ini deps, fix bugs
new a9594b965b venv support for agent, update notebooks, show tables as
pandas df, update dir refs, fix bugs.
new 1046150be6 make settings.ini lean, add runtime picker {by cluster,
category}. change agent base dir.
new 47d882e396 add pre-submission validator, update storage dir, take
CONNECTION_SVC_URL and FILEMGR_SVC_URL from settings.ini, cleanup runtime.py,
add fallback apis to airavata.py, rearrange files, setup file ul/dl apis,
improve ux, update notebooks, add agent scripts, refine code, fix bugs
new 599fba45fd fix bug in code execution, remove jupyter kernel start from
agent add support to cold-start analysis agents reset changes to
sftp_file_handling_client update notebooks remove verbose log from remote code
execution separate python env creation and code execution steps. always return
stdout+err for command/script executions lock agent to python 3.12 and update
pyproject.toml update file listing and python execution cmds
new fa6a4207a0 bump version to 0.0.16 add AlphaFold2 and Gaussian
applications update realm from 10000000 -> default add GROMACS and AMBER to MD
SDK
new 83052b074d choose group/project from API, silent plan launch,
add_replica() -> create_task(), display task state, planid and taskid, improve
messaging
new 8061e070b5 add back kernel launcher to agent
new ca369fc700 refine Makefiles, move app-scripts to agent-framework/, fix
bugs in agent.go and sample Dockerfile
new d7d5275990 regenerate thrift specs
new 251edd3890 cleanup airavata_sdk wrappers, error-handling in
airavata_experiments
new c3273418ba add type-hinting imports to __init__ files
new 86425b63dd cleanup imports, fix bugs found by type checker
new 118b1dcc18 enabled micromamba base when starting the kernel
new de6c7f04af fix bugs in airavata-jupyter-magic package
new 9776da5d14 fix dependency issue in cyberfaces agent
new 8b9cfeae02 organize code, add other deployment files, partially redo
airavata_jupyter_magic for runtime switching
new 56bee085dc refine code flow in airavata_jupyter_magic. bump version to
1.0.5, update notebook, fix bugs
new 94319b5951 updated notebooks
new 7716162705 rename platform x86_64 -> amd64. fix issues in cyberfaces
dockerfile. update notebooks. move environment files.
new c96c793730 updated the agent dependencies
new d3c191c8f3 gkeyll agent image and notebook sample
new 5f42822a16 updated the gkeyll notebook script
The 31 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.../airavata-python-sdk/.gitignore | 8 +
.../airavata-python-sdk/airavata/__init__.py | 4 +
.../airavata/api/Airavata-remote | 4 +-
.../airavata-python-sdk/airavata/api/Airavata.py | 6252 +-
.../airavata-python-sdk/airavata/api/__init__.py | 5 +
.../airavata-python-sdk/airavata/api/constants.py | 8 +-
.../airavata/api/credential/__init__.py | 4 +
.../credential/store/CredentialStoreService-remote | 4 +-
.../api/credential/store/CredentialStoreService.py | 349 +-
.../airavata/api/credential/store/__init__.py | 5 +
.../airavata/api/credential/store/constants.py | 8 +-
.../api/credential/store/error/__init__.py | 5 +
.../api/credential/store/error/constants.py | 8 +-
.../airavata/api/credential/store/error/ttypes.py | 12 +-
.../airavata/api/credential/store/ttypes.py | 8 +-
.../airavata/api/error/__init__.py | 5 +
.../airavata/api/error/constants.py | 8 +-
.../airavata/api/error/ttypes.py | 97 +-
.../api/sharing/SharingRegistryService-remote | 4 +-
.../airavata/api/sharing/SharingRegistryService.py | 1424 +-
.../airavata/api/sharing/__init__.py | 5 +
.../airavata/api/sharing/constants.py | 8 +-
.../airavata/api/sharing/ttypes.py | 8 +-
.../airavata-python-sdk/airavata/api/ttypes.py | 8 +-
.../airavata-python-sdk/airavata/base/__init__.py | 4 +
.../airavata/base/api/BaseAPI-remote | 4 +-
.../airavata/base/api/BaseAPI.py | 22 +-
.../airavata/base/api/__init__.py | 5 +
.../airavata/base/api/constants.py | 8 +-
.../airavata/base/api/ttypes.py | 8 +-
.../airavata-python-sdk/airavata/model/__init__.py | 5 +
.../airavata/model/appcatalog/__init__.py | 4 +
.../appcatalog/accountprovisioning/__init__.py | 5 +
.../appcatalog/accountprovisioning/constants.py | 8 +-
.../model/appcatalog/accountprovisioning/ttypes.py | 56 +-
.../model/appcatalog/appdeployment/__init__.py | 5 +
.../model/appcatalog/appdeployment/constants.py | 8 +-
.../model/appcatalog/appdeployment/ttypes.py | 91 +-
.../model/appcatalog/appinterface/__init__.py | 5 +
.../model/appcatalog/appinterface/constants.py | 8 +-
.../model/appcatalog/appinterface/ttypes.py | 28 +-
.../model/appcatalog/computeresource/__init__.py | 5 +
.../model/appcatalog/computeresource/constants.py | 8 +-
.../model/appcatalog/computeresource/ttypes.py | 426 +-
.../model/appcatalog/gatewaygroups/__init__.py | 5 +
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.../model/appcatalog/gatewayprofile/__init__.py | 5 +
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.../model/appcatalog/gatewayprofile/ttypes.py | 94 +-
.../appcatalog/groupresourceprofile/__init__.py | 5 +
.../appcatalog/groupresourceprofile/constants.py | 8 +-
.../appcatalog/groupresourceprofile/ttypes.py | 142 +-
.../model/appcatalog/parallelism/__init__.py | 5 +
.../model/appcatalog/parallelism/constants.py | 8 +-
.../model/appcatalog/parallelism/ttypes.py | 27 +-
.../airavata/model/appcatalog/parser/__init__.py | 5 +
.../airavata/model/appcatalog/parser/constants.py | 8 +-
.../airavata/model/appcatalog/parser/ttypes.py | 145 +-
.../model/appcatalog/storageresource/__init__.py | 5 +
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.../model/appcatalog/storageresource/ttypes.py | 26 +-
.../appcatalog/userresourceprofile/__init__.py | 5 +
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.../model/appcatalog/userresourceprofile/ttypes.py | 68 +-
.../airavata/model/application/__init__.py | 4 +
.../airavata/model/application/io/__init__.py | 5 +
.../airavata/model/application/io/constants.py | 8 +-
.../airavata/model/application/io/ttypes.py | 115 +-
.../airavata/model/commons/__init__.py | 5 +
.../airavata/model/commons/constants.py | 8 +-
.../airavata/model/commons/ttypes.py | 40 +-
.../airavata/model/constants.py | 8 +-
.../airavata/model/credential/__init__.py | 4 +
.../airavata/model/credential/store/__init__.py | 5 +
.../airavata/model/credential/store/constants.py | 8 +-
.../airavata/model/credential/store/ttypes.py | 118 +-
.../airavata/model/data/__init__.py | 4 +
.../airavata/model/data/movement/__init__.py | 5 +
.../airavata/model/data/movement/constants.py | 8 +-
.../airavata/model/data/movement/ttypes.py | 157 +-
.../airavata/model/data/replica/__init__.py | 5 +
.../airavata/model/data/replica/constants.py | 8 +-
.../airavata/model/data/replica/ttypes.py | 134 +-
.../airavata/model/dbevent/__init__.py | 5 +
.../airavata/model/dbevent/constants.py | 8 +-
.../airavata/model/dbevent/ttypes.py | 130 +-
.../airavata/model/experiment/__init__.py | 5 +
.../airavata/model/experiment/constants.py | 8 +-
.../airavata/model/experiment/ttypes.py | 212 +-
.../airavata/model/group/__init__.py | 5 +
.../airavata/model/group/constants.py | 8 +-
.../airavata/model/group/ttypes.py | 64 +-
.../airavata/model/job/__init__.py | 5 +
.../airavata/model/job/constants.py | 8 +-
.../airavata/model/job/ttypes.py | 36 +-
.../airavata/model/messaging/__init__.py | 4 +
.../airavata/model/messaging/event/__init__.py | 5 +
.../airavata/model/messaging/event/constants.py | 8 +-
.../airavata/model/messaging/event/ttypes.py | 301 +-
.../airavata/model/process/__init__.py | 5 +
.../airavata/model/process/constants.py | 8 +-
.../airavata/model/process/ttypes.py | 76 +-
.../airavata/model/scheduling/__init__.py | 5 +
.../airavata/model/scheduling/constants.py | 8 +-
.../airavata/model/scheduling/ttypes.py | 42 +-
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.../airavata/model/sharing/__init__.py | 5 +
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.../airavata/model/sharing/ttypes.py | 362 +-
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.../airavata/model/status/ttypes.py | 234 +-
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.../airavata/model/tenant/ttypes.py | 94 +-
.../airavata-python-sdk/airavata/model/ttypes.py | 8 +-
.../airavata/model/user/__init__.py | 5 +
.../airavata/model/user/constants.py | 8 +-
.../airavata/model/user/ttypes.py | 269 +-
.../airavata/model/workflow/__init__.py | 5 +
.../airavata/model/workflow/constants.py | 8 +-
.../airavata/model/workflow/ttypes.py | 348 +-
.../airavata/model/workspace/__init__.py | 5 +
.../airavata/model/workspace/constants.py | 8 +-
.../airavata/model/workspace/ttypes.py | 192 +-
.../airavata/service/__init__.py | 4 +
.../airavata/service/profile/__init__.py | 5 +
.../airavata/service/profile/constants.py | 8 +-
.../service/profile/groupmanager/__init__.py | 4 +
.../groupmanager/cpi/GroupManagerService-remote | 4 +-
.../groupmanager/cpi/GroupManagerService.py | 360 +-
.../service/profile/groupmanager/cpi/__init__.py | 5 +
.../service/profile/groupmanager/cpi/constants.py | 8 +-
.../profile/groupmanager/cpi/error/__init__.py | 5 +
.../profile/groupmanager/cpi/error/constants.py | 8 +-
.../profile/groupmanager/cpi/error/ttypes.py | 12 +-
.../service/profile/groupmanager/cpi/ttypes.py | 8 +-
.../airavata/service/profile/iam/__init__.py | 4 +
.../airavata/service/profile/iam/admin/__init__.py | 4 +
.../service/profile/iam/admin/services/__init__.py | 4 +
.../iam/admin/services/cpi/IamAdminServices-remote | 4 +-
.../iam/admin/services/cpi/IamAdminServices.py | 416 +-
.../profile/iam/admin/services/cpi/__init__.py | 5 +
.../profile/iam/admin/services/cpi/constants.py | 8 +-
.../iam/admin/services/cpi/error/__init__.py | 5 +
.../iam/admin/services/cpi/error/constants.py | 8 +-
.../profile/iam/admin/services/cpi/error/ttypes.py | 12 +-
.../profile/iam/admin/services/cpi/ttypes.py | 8 +-
.../airavata/service/profile/tenant/__init__.py | 4 +
.../profile/tenant/cpi/TenantProfileService-remote | 4 +-
.../profile/tenant/cpi/TenantProfileService.py | 190 +-
.../service/profile/tenant/cpi/__init__.py | 5 +
.../service/profile/tenant/cpi/constants.py | 8 +-
.../service/profile/tenant/cpi/error/__init__.py | 5 +
.../service/profile/tenant/cpi/error/constants.py | 8 +-
.../service/profile/tenant/cpi/error/ttypes.py | 12 +-
.../airavata/service/profile/tenant/cpi/ttypes.py | 8 +-
.../airavata/service/profile/ttypes.py | 8 +-
.../airavata/service/profile/user/__init__.py | 4 +
.../profile/user/cpi/UserProfileService-remote | 4 +-
.../service/profile/user/cpi/UserProfileService.py | 198 +-
.../airavata/service/profile/user/cpi/__init__.py | 5 +
.../airavata/service/profile/user/cpi/constants.py | 8 +-
.../service/profile/user/cpi/error/__init__.py | 5 +
.../service/profile/user/cpi/error/constants.py | 8 +-
.../service/profile/user/cpi/error/ttypes.py | 12 +-
.../airavata/service/profile/user/cpi/ttypes.py | 8 +-
.../airavata_experiments/__init__.py | 180 +
.../airavata_experiments/airavata.py | 800 +
.../auth}/__init__.py | 15 +
.../airavata_experiments/auth/device_auth.py | 186 +
.../airavata_experiments/base.py | 133 +
.../utils => airavata_experiments/md}/__init__.py | 10 +
.../airavata_experiments/md/applications.py | 258 +
.../airavata_experiments/plan.py | 199 +
.../airavata_experiments/runtime.py | 274 +
.../airavata_experiments/scripter.py | 144 +
.../airavata_experiments/sftp.py | 122 +
.../airavata_experiments/task.py | 106 +
.../airavata_sdk/clients/api_server_client.py | 7231 +-
.../clients/credential_store_client.py | 47 +-
.../airavata_sdk/clients/file_handling_client.py | 18 +-
.../airavata_sdk/clients/group_manager_client.py | 216 +-
.../airavata_sdk/clients/iam_admin_client.py | 239 +-
.../airavata_sdk/clients/keycloak_token_fetcher.py | 100 +-
.../clients/sftp_file_handling_client.py | 23 +-
.../clients/sharing_registry_client.py | 916 +-
.../airavata_sdk/clients/tenant_profile_client.py | 126 +-
.../airavata_sdk/clients/user_profile_client.py | 137 +-
.../clients/utils/api_server_client_util.py | 41 +-
.../clients/utils/data_model_creation_util.py | 93 +-
.../clients/utils/experiment_handler_util.py | 79 +-
.../samples/api_server_client_samples.py | 17 +-
.../samples/create_launch_echo_experiment.py | 43 +-
.../samples/create_launch_gaussian_experiment.py | 50 +-
.../airavata_sdk/samples/file_utils.py | 1 +
.../samples/group_manager_client_samples.py | 8 +-
.../samples/iam_admin_client_samples.py | 5 +-
.../airavata_sdk/samples/metadata_fetcher.py | 16 +-
.../samples/sharing_registry_client_samples.py | 6 +-
.../samples/tenant_profile_client_samples.py | 5 +-
.../samples/user_profile_client_samples.py | 8 +-
.../airavata_sdk/transport/settings.py | 56 +-
.../airavata_sdk/transport/utils.py | 317 +-
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369 files changed, 163602 insertions(+), 18252 deletions(-)
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modules/agent-framework/airavata-jupyter-magic}/__init__.py (100%)
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modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py
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modules/agent-framework/{airavata-agent/jupyter/deployments/i-guide/jupyterlab/labconfig
=> airavata-jupyter-magic}/device_auth.py (98%)
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modules/agent-framework/deployments/jupyterhub/data/md_demo}/settings.ini (85%)
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/data/b4pull.pdb
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/data/b4pull.restart.vel
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/data/par_all36m_prot.prm
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/data/pull_cpu.conf
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/data/pull_gpu.conf
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/data/structure.pdb
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/data/structure.psf
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop}/settings.ini
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_cpu.ipynb
(94%)
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modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_gpu.ipynb
(93%)
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modules/agent-framework/deployments}/jupyterhub/docker-compose.yaml (85%)
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modules/agent-framework/deployments}/jupyterhub/jupyterhub_config.py (93%)
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modules/agent-framework/deployments}/jupyterhub/nginx-conf (100%)
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}/proto/agent-communication.proto (100%)
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}/proto/airavata-fuse.proto (100%)
